Abstract
The pathway for RNA interference is widespread in metazoans and participates in numerous cellular tasks, from gene silencing to chromatin remodeling and protection against retrotransposition. The unicellular eukaryote Trypanosoma cruzi is missing the canonical RNAi pathway and is unable to induce RNAi-related processes. To further understand alternative RNA pathways operating in this organism, we have performed deep sequencing and genome-wide analyses of a size-fractioned cDNA library (16–61 nt) from the epimastigote life stage. Deep sequencing generated 582,243 short sequences of which 91% could be aligned with the genome sequence. About 95–98% of the aligned data (depending on the haplotype) corresponded to small RNAs derived from tRNAs, rRNAs, snRNAs and snoRNAs. The largest class consisted of tRNA-derived small RNAs which primarily originated from the 3′ end of tRNAs, followed by small RNAs derived from rRNA. The remaining sequences revealed the presence of 92 novel transcribed loci, of which 79 did not show homology to known RNA classes.
Highlights
Trypanosoma cruzi is a protozoan parasite and the causative agent of Chagas’ disease, which has substantial health and socioeconomic impact in Latin America [1]
For reads with a single alignment location, 97.4% (378,446/388,551) of the reads in non-Esmeraldo and 96.7% (157,280/162,622) in Esmeraldo were found to correspond to small ncRNAs derived from tRNA, rRNA, snRNA and Small nucleolar RNAs (snoRNAs) (Table 3). tRNA-derived small RNAs was found to be the most abundant type in the library, composing at least 65.3% (380,191/582,243) of the total sequence data, which we further describe
We found no correlation between the observed tRNA-derived small RNAs (tsRNA) expression and the amino acid usage (Pearson’s correlation, r = 20.05), nor was there a correlation between the genomic copy number of tRNA and tsRNA expression (Pearson’s correlation, r = 0.08), suggesting that T. cruzi tsRNAs are not random degradation products from tRNA turnover
Summary
Trypanosoma cruzi is a protozoan parasite and the causative agent of Chagas’ disease, which has substantial health and socioeconomic impact in Latin America [1]. The genome of T. cruzi strain CL Brener is complex in terms of sequence repetitiveness and is a hybrid between two diverged haplotypes, named non-Esmeraldo-like and Esmeraldo-like: we refer to them here as non-Esmeraldo and Esmeraldo. Taken together, both haplotypes [2] sum up to approximately 110 Mb distributed over at least 80 chromosomes [3]. The genome of a different, non-hybrid strain named Sylvio X10 was recently sequenced and partially assembled, showing a core gene content highly similar to CL Brener [5]
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